A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the qbic-pipelines/variantconsensus analysis pipeline.
/Users/famke/01-pm4onco/repositories/variantconsensus/.nf-test/tests/f05c1aa129c204b7d145bd98dae2f44c/work/b0/af4323d4b7fee694c099c629f417b7
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| FILTER_INDELS | bcftools | 1.21 |
| FILTER_SNPS | bcftools | 1.21 |
| Workflow | Nextflow | 24.10.4 |
| qbic-pipelines/variantconsensus | v1.0.0dev |
qbic-pipelines/variantconsensus Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/qbic-pipelines/variantconsensus
Methods
Data was processed using qbic-pipelines/variantconsensus v1.0.0dev of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v24.10.4 (Di Tommaso et al., 2017) with the following command:
nextflow -quiet -log /Users/famke/01-pm4onco/repositories/variantconsensus/.nf-test/tests/f05c1aa129c204b7d145bd98dae2f44c/meta/nextflow.log run /Users/famke/01-pm4onco/repositories/variantconsensus/tests/../main.nf -c /Users/famke/01-pm4onco/repositories/variantconsensus/nextflow.config -c /Users/famke/01-pm4onco/repositories/variantconsensus/tests/nextflow.config -c /Users/famke/01-pm4onco/repositories/variantconsensus/conf/test.config -params-file /Users/famke/01-pm4onco/repositories/variantconsensus/.nf-test/tests/f05c1aa129c204b7d145bd98dae2f44c/meta/params.json -ansi-log false -profile test,docker -with-trace /Users/famke/01-pm4onco/repositories/variantconsensus/.nf-test/tests/f05c1aa129c204b7d145bd98dae2f44c/meta/trace.csv -w /Users/famke/01-pm4onco/repositories/variantconsensus/.nf-test/tests/f05c1aa129c204b7d145bd98dae2f44c/work
References
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
Notes:
- If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
qbic-pipelines/variantconsensus Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/qbic-pipelines/variantconsensus
Input/output options
- input
- /Users/famke/01-pm4onco/repositories/variantconsensus/tests/test-samplesheet.csv
- outdir
- /Users/famke/01-pm4onco/repositories/variantconsensus/.nf-test/tests/f05c1aa129c204b7d145bd98dae2f44c/output
Institutional config options
- config_profile_description
- Minimal test dataset to check pipeline function
- config_profile_name
- Test profile
Generic options
- pipelines_testdata_base_path
- ${projectDir}/tests/
- trace_report_suffix
- 2025-04-09_16-46-31
Core Nextflow options
- configFiles
- /Users/famke/01-pm4onco/repositories/variantconsensus/nextflow.config, /Users/famke/01-pm4onco/repositories/variantconsensus/nextflow.config, /Users/famke/01-pm4onco/repositories/variantconsensus/tests/nextflow.config, /Users/famke/01-pm4onco/repositories/variantconsensus/conf/test.config
- containerEngine
- docker
- launchDir
- /Users/famke/01-pm4onco/repositories/variantconsensus/.nf-test/tests/f05c1aa129c204b7d145bd98dae2f44c
- profile
- test,docker
- projectDir
- /Users/famke/01-pm4onco/repositories/variantconsensus
- runName
- condescending_neumann
- userName
- famke
- workDir
- /Users/famke/01-pm4onco/repositories/variantconsensus/.nf-test/tests/f05c1aa129c204b7d145bd98dae2f44c/work